Multiplex assay for the detection of citrus pathogens

ABSTRACT

The present invention provides methods and compositions for detecting multiple citrus pathogens using a multiplex branched DNA signal amplification reaction.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority benefit to U.S. provisional application No. 61/673,090, filed Jul. 18, 2012, which application is herein incorporated by reference for all purposes.

STATEMENT OF GOVERNMENTAL SUPPORT

This invention was made with Government support under Grant Nos. 58-5302-1-119 and 58-5302-1-226, awarded by the U.S. Department of Agriculture. The Government has certain rights in this invention.

REFERENCE TO A “SEQUENCE LISTING,” A TABLE, OR A COMPUTER PROGRAM LISTING APPENDIX SUBMITTED AS AN ASCII TEXT FILE

The Sequence Listing written in file -2118-1.TXT, created on Aug. 21, 2013, 57,344 bytes, machine format IBM-PC, MS-Windows operating system, is hereby incorporated by reference in its entirety for all purposes.

BACKGROUND OF THE INVENTION

Citrus is susceptible to numerous disease caused by plant pathogens. There is a need for efficient and sensitive methods of detecting pathogens.

The method of the present invention provides a method for the detection of nine citrus pathogens in a single sample using a multiplex branched signal amplification reaction. The present invention thus provides an accurate, efficient, and quick method of detecting multiple citrus pathogens that is also suitable for high throughput screenings.

BRIEF SUMMARY OF THE INVENTION

The present invention provides methods and kits for detecting up to nine citrus pathogens where the pathogens are Citrus tristeza virus (CTV) universal, CTV genotype T30 and CTV genotype VT; Citrus psorosis virus (CPsV); Citrus tatter leaf virus (CTLV); Citrus leaf blotch virus (CLBV); Citrus exocortis viroid (CEVd); Hop stunt viroid (HSVd); and Citrus leprosis virus (CiLV). In some embodiments, the methods and kits additionally comprise components for detecting a housekeeping citrus gene, NADH dehydrogenase gene (Nad5) as an internal control.

In some aspects, the invention provides the following illustrative embodiments:

Embodiment 1

A method for detecting the presence of at least one citrus pathogen selected from Citrus tristeza virus (CTV) universal, CTV genotype T30, CTV genotype VT, Citrus psorosis virus, Citrus tatter leaf virus, Citrus leaf blotch virus, Citrus exocortis viroid, Hop stunt viroid, or Citrus leprosis virus in a plant sample, the method comprising:

extracting RNA from said sample;

performing a multiplex branched DNA signal amplification reaction; wherein the reaction comprises at least one capture extender probe and at least one label extender probe that targets the pathogen, wherein the at least one capture extender probe and the at least one label extender probe each comprises at least 8, 9, or 10 contiguous nucleotide of a probe sequence shown in Table 1; and detecting the presence or absence of a signal above background, wherein the presence of the signal is indicative of the presence of the pathogen.

Embodiment 2

The method of embodiment 1, wherein the reaction comprises multiple capture extender probes and multiple label extender probes that target the pathogen, wherein each of the multiple capture extender probes and multiple label extender probes that target the pathogen comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence as shown in Table 1.

Embodiment 3

The method of embodiment 1 or 2, wherein each of the probes that target the pathogen comprises a probe sequence set forth in Table 1.

Embodiment 4

The method of embodiment 1, further comprising detecting the presence or absence of a second pathogen selected from Citrus tristeza virus (CTV) universal, CTV genotype T30, CTV genotype VT, Citrus psorosis virus, Citrus tatter leaf virus, Citrus leaf blotch virus, Citrus exocortis viroid, Hop stunt viroid, or Citrus leprosis virus in the plant sample, wherein the reaction comprises at least one capture extender probe and at least one label extender probe that target the second pathogen, wherein the capture extender probe and the label extender probe that target the second pathogen each comprise at least 8, 9, or 10 contiguous nucleotides of a probe sequence as shown in Table 1.

Embodiment 5

The method of embodiment 4, wherein the reaction comprises multiple capture extender probes and multiple label extender probes that target the second pathogen, wherein each of the multiple capture extender probes and multiple label extender probes that target the second pathogen comprise at least 8, 9, or 10 contiguous nucleotides of a probe sequence as shown in Table 1.

Embodiment 6

The method of embodiment 4 or 5, wherein each of the probes that target the second pathogen comprises a probe sequence as shown in Table 1.

Embodiment 7

The method of embodiment 4, further comprising detecting the presence or absence of a third, fourth, fifth, sixth, seventh, or eighth pathogen selected from Citrus tristeza virus (CTV) universal, CTV genotype T30, CTV genotype VT, Citrus psorosis virus, Citrus tatter leaf virus, Citrus leaf blotch virus, Citrus exocortis viroid, Hop stunt viroid, or Citrus leprosis virus in the plant sample, wherein the reaction comprises at least one capture extender probe and at least one label extender probe that target the third, fourth, fifth, sixth, seventh, or eighth pathogen, wherein the capture extender probe and the label extender probe each comprise at least 8, 9, or 10 contiguous nucleotides of a probe sequence as shown in Table 1.

Embodiment 8

The method of embodiment 7, wherein the reaction comprises multiple capture extender probes and multiple label extender probes that target the third, fourth, fifth, sixth, seventh, or eighth pathogen, wherein each of the multiple probes comprises at least 8, 9, or contiguous nucleotides of a probe sequence as shown in Table 1.

Embodiment 9

The method of embodiment 7 or 8, wherein each of the probes that target the third, fourth, fifth, sixth, seventh, or eighth pathogen comprises a probe sequence as shown in Table 1.

Embodiment 10

The method of embodiment 1, comprising detecting the presence or absence of the nine pathogens Citrus tristeza virus (CTV) universal, CTV genotype T30, CTV genotype VT, Citrus psorosis virus, Citrus tatter leaf virus, Citrus leaf blotch virus, Citrus exocortis viroid, Hop stunt viroid, and Citrus leprosis virus in the plant sample, wherein for each of the nine pathogens, the reaction comprises a capture extender probe and a label extender probe, wherein each capture extender probe and each label extender probe comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence as shown in Table 1.

Embodiment 11

The method of embodiment 10, wherein the reaction comprises multiple capture extender probes and multiple label extender probes that target each of the nine pathogens, wherein each of the multiple capture extender probes and each of the multiple label extender probes comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence shown in Table 1.

Embodiment 12

The method of embodiment 10 or 11, wherein each of the probes that target the nine pathogens comprises a probe sequence shown in Table 1.

Embodiment 13

The method of any one of embodiments 1 to 12, wherein the reaction comprises at least one blocking probe listed in Table 1 for the corresponding pathogen.

Embodiment 14

The method of any one of embodiment 1 to 12, wherein the reaction comprises all of the blocking probes listed in Table 1.

Embodiment 15

The method of any one of embodiments 1 to 14, wherein the reaction further comprises using one of the capture extender probes and one of the label extender probes for Nad5 listed in Table 1.

Embodiment 16

The method of embodiment 15, wherein the reaction comprises using all of the label extender probes and all of the capture extender probes for Nad5 listed in Table 1.

Embodiment 17

The method of any one of embodiments 1 to 16, wherein the plant sample is from seed, foliage, limbs, trunk, bark, rootstock, fruit, germplasm, propagule, cuttings, or budwood.

Embodiment 18

A reaction mixture for detecting the presence of at least one citrus pathogen selected from Citrus tristeza virus (CTV) universal, CTV genotype T30, CTV genotype VT, Citrus psorosis virus, Citrus tatter leaf virus, Citrus leaf blotch virus, Citrus exocortis viroid, Hop stunt viroid, or Citrus leprosis virus in a plant sample, wherein the reaction mixture comprises at least one capture extender probe and at least one label extender probe that target the pathogen, where the at least one capture extender probe and at least one label extender probe comprises 8, 9, or 10 contiguous nucleotide of a probe sequence as shown in Table 1.

Embodiment 19

The reaction mixture of embodiment 18, wherein the reaction comprises multiple capture extender probes and multiple label extender probes that target the pathogen, wherein each of the multiple capture extender probes and multiple label extender probes comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence as shown in Table 1.

Embodiment 20

The reaction mixture of embodiment 18 or 19, wherein each of the probes that target the pathogen comprises a probe sequence set forth in Table 1.

Embodiment 21

The reaction mixture of embodiment 18, further comprising at least one capture extender probe and at least one label extender probe that target a second pathogen selected from Citrus tristeza virus (CTV) universal, CTV genotype T30, CTV genotype VT, Citrus psorosis virus, Citrus tatter leaf virus, Citrus leaf blotch virus, Citrus exocortis viroid, Hop stunt viroid, or Citrus leprosis virus, wherein the capture extender probe and the label extender probe that target the second pathogen each comprise at least 8, 9, or 10 contiguous nucleotides of a probe sequence as shown in Table 1.

Embodiment 22

The reaction mixture of embodiment 21, wherein the reaction comprises multiple capture extender probes and multiple label extender probes that target the second pathogen, wherein each of the multiple capture extender probes and multiple label extender probes comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence as shown in Table 1.

Embodiment 23

The reaction mixture of embodiment 21 or 22, wherein each of the probes that target the second pathogen comprises a probe sequence as shown in Table 1.

Embodiment 24

The reaction mixture of embodiment 21, further comprising at least one capture extender probe and at least one label extender probe that target a third, fourth, fifth, sixth, seventh, or eighth pathogen selected from Citrus tristeza virus (CTV) universal, CTV genotype T30, CTV genotype VT, Citrus psorosis virus, Citrus tatter leaf virus, Citrus leaf blotch virus, Citrus exocortis viroid, Hop stunt viroid, or Citrus leprosis virus, wherein the capture extender probe and the label extender probe each comprise at least 8, 9, or 10 contiguous nucleotides of a probe sequence as shown in Table 1.

Embodiment 25

The reaction mixture of embodiment 24, wherein the reaction comprises multiple capture extender probes and multiple label extender probes that target the third, fourth, fifth, sixth, seventh, or eighth pathogen, wherein each of the multiple probes comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence as shown in Table 1.

Embodiment 26

The reaction mixture of embodiment 24 or 25, wherein each of the probes that target the third, fourth, fifth, sixth, seventh, or eighth pathogen comprises a probe sequence as shown in Table 1.

Embodiment 27

The reaction mixture of embodiment 18, comprising a capture extender probe and a label extender probe for each of the nine pathogens Citrus tristeza virus (CTV) universal, CTV genotype T30, CTV genotype VT, Citrus psorosis virus, Citrus tatter leaf virus, Citrus leaf blotch virus, Citrus exocortis viroid, Hop stunt viroid, and Citrus leprosis virus, wherein each capture extender probe and each label extender probe comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence as shown in Table 1.

Embodiment 28

The reaction mixture of embodiment 27, comprising multiple capture extender probes and multiple label extender probes that target each of the nine pathogens, wherein each of the multiple capture extender probes and each of the multiple label extender probes comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence shown in Table 1.

Embodiment 29

The reaction mixture of embodiment 27 or 28, wherein each of the probes that target the nine pathogens comprises a probe sequence shown in Table 1.

Embodiment 30

The reaction mixture of any one of embodiments 18 to 29, wherein the reaction comprises at least one blocking probe listed in Table 1 for the corresponding pathogen.

Embodiment 31

The reaction mixture of any one of embodiments 18 to 29, wherein the reaction mixture comprises all of the blocking probes listed in Table 1.

Embodiment 32

The reaction mixture of any one of embodiments 18 to 31, wherein the reaction mixture further comprises one of the capture extender probes and one of the label extender probes for Nad5 listed in Table 1, or all of the capture extender probes and all of the label extender probes for Nad5 listed in Table 1.

Embodiment 33

A kit mixture for detecting the presence of at least one citrus pathogen selected from Citrus tristeza virus (CTV) universal, CTV genotype T30, CTV genotype VT, Citrus psorosis virus, Citrus tatter leaf virus, Citrus leaf blotch virus, Citrus exocortis viroid, Hop stunt viroid, or Citrus leprosis virus in a plant sample, wherein the kit comprises at least one capture extender probe and at least one label extender probe that target the pathogen, where the at least one capture extender probe and at least one label extender probe comprises 8, 9, or 10 contiguous nucleotide of a probe sequence as shown in Table 1.

Embodiment 34

The kit of embodiment 33, wherein the kit comprises multiple capture extender probes and multiple label extender probes that target the pathogen, wherein each of the multiple capture extender probes and multiple label extender probes comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence as shown in Table 1.

Embodiment 35

The kit of embodiment 33 or 34, wherein each of the probes that target the pathogen comprises a probe sequence set forth in Table 1.

Embodiment 36

The kit of embodiment 33, further comprising at least one capture extender probe and at least one label extender probe that target a second pathogen selected from Citrus tristeza virus (CTV) universal, CTV genotype T30, CTV genotype VT, Citrus psorosis virus, Citrus tatter leaf virus, Citrus leaf blotch virus, Citrus exocortis viroid, Hop stunt viroid, or Citrus leprosis virus, wherein the capture extender probe and the label extender probe that target the second pathogen each comprise at least 8, 9, or 10 contiguous nucleotides of a probe sequence as shown in Table 1.

Embodiment 37

The kit of embodiment 36, wherein the reaction comprises multiple capture extender probes and multiple label extender probes that target the second pathogen, wherein each of the multiple capture extender probes and multiple label extender probes comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence as shown in Table 1.

Embodiment 38

The kit of embodiment 36 or 37, wherein each of the probes that target the second pathogen comprises a probe sequence as shown in Table 1.

Embodiment 39

The kit of embodiment 36, further comprising at least one capture extender probe and at least one label extender probe that target a third, fourth, fifth, sixth, seventh, or eighth pathogen selected from Citrus tristeza virus (CTV) universal, CTV genotype T30, CTV genotype VT, Citrus psorosis virus, Citrus tatter leaf virus, Citrus leaf blotch virus, Citrus exocortis viroid, Hop stunt viroid, or Citrus leprosis virus, wherein the capture extender probe and the label extender probe each comprise at least 8, 9, or 10 contiguous nucleotides of a probe sequence as shown in Table 1.

Embodiment 40

The kit of embodiment 39, wherein the kit comprises multiple capture extender probes and multiple label extender probes that target the third, fourth, fifth, sixth, seventh, or eighth pathogen, wherein each of the multiple probes comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence as shown in Table 1.

Embodiment 41

The kit of embodiment 39 or 40, wherein each of the probes that target the third, fourth, fifth, sixth, seventh, or eighth pathogen comprises a probe sequence as shown in Table 1.

Embodiment 42

The kit of embodiment 33, comprising a capture extender probe and a label extender probe for each of the nine pathogens Citrus tristeza virus (CTV) universal, CTV genotype T30, CTV genotype VT, Citrus psorosis virus, Citrus tatter leaf virus, Citrus leaf blotch virus, Citrus exocortis viroid, Hop stunt viroid, and Citrus leprosis virus, wherein each capture extender probe and each label extender probe comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence as shown in Table 1.

Embodiment 43

The kit of embodiment 42, comprising multiple capture extender probes and multiple label extender probes that target each of the nine pathogens, wherein each of the multiple capture extender probes and each of the multiple label extender probes comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence shown in Table 1.

Embodiment 44

The kit of embodiment 42 or 43, wherein each of the probes that target the nine pathogens comprises a probe sequence shown in Table 1.

Embodiment 45

The kit of any one of embodiments 33 to 44, wherein the kit comprises at least one blocking probe listed in Table 1 for the corresponding pathogen.

Embodiment 46

The kit of any one of embodiments 33 to 44, wherein the kit comprises all of the blocking probes listed in Table 1.

Embodiment 47

The kit of any one of embodiments 33 to 46, wherein the kit further comprises one of the capture extender probes and one of the label extender probes for Nad5 listed in Table 1, or all of the capture extender probes and all of the label extender probes for Nad5 listed in Table 1.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 provides illustrative data showing a 10-Plex reaction detecting citrus pathogens.

FIG. 2 provides illustrative data showing universal and genotype-specific detection of citrus pathogen CTV.

FIG. 3 provides illustrative data showing specific detection of citrus viroids CEVd and HSVd.

DETAILED DESCRIPTION OF THE INVENTION

As used herein, a “probe that targets a pathogen” refers to a nucleotide sequence that hybridizes to a desired region of a target nucleic acid in the pathogen.

The term “hybridization” refers to the formation of a duplex structure by two single stranded nucleic acids due to complementary base pairing. Hybridization can occur between exactly complementary nucleic acid strands or between nucleic acid strands that contain minor regions of mismatch. As used herein, the term “substantially complementary” refers to sequences that are complementary except for minor regions of mismatch. Typically, the total number of mismatched nucleotides over a hybridizing region is not more than 3 nucleotides for sequences about 15 nucleotides in length.

The term “probe” refers to an oligonucleotide that selectively hybridizes to a target nucleic acid under suitable conditions. A hybridization assay carried out using a probe under sufficiently stringent hybridization conditions enables the selective detection of a specific target sequence comprising the region of interest of a pathogen nucleic acid. The probe hybridizing region is preferably from about 10 to about 35 nucleotides in length. In some embodiments, the probe hybridizing region is 15 to about 35 nucleotides in length. The use of modified bases or base analogues which affect the hybridization stability, which are well known in the art, may enable the use of shorter or longer probes with comparable stability.

The term “target sequence” or “target region” refers to a region of a nucleic acid in a pathogen of interest to which a probe to the pathogen binds.

A “capture extender probe” or “CE probe” as used here is a polynucleotide that is capable of hybridizing to a nucleic acid of interest from a citrus pathogen and to a capture probe. The capture extender probe has a first polynucleotide sequence that is complementary to a capture probe, and a second polynucleotide sequence, e.g., a sequence as shown in Table 1, which is complementary to a citrus pathogen nucleic acid as described herein. The capture probe is typically immobilized to a solid support, including but not limited to a chip (e.g., an array), well, bead, or other solid support or matrix.

A “label extender probe” or “LE” as used here is a polynucleotide that is capable of hybridizing to a nucleic acid of interest from a pathogen and to a label probe system. The label extender probe has a first polynucleotide sequence that is complementary to a polynucleotide sequence of the label probe system and a second polynucleotide sequence, e.g., a sequence as shown in Table 1, which is complementary to a citrus pathogen as described herein. The signal-amplifying probe in the present invention typically comprises branched DNA, e.g., may include a pre-Amplifier probe, an Amplifier probe, and a Label probe.

Introduction

The present invention provides methods to diagnose infection with citrus pathogens. In some embodiments, the methods can be used in high-throughput screenings of thousands of plant samples in regulatory and research programs. Branched DNA technology (bDNA) employs a sandwich nucleic acid hybridization assay for nucleic acid detection and quantification that amplifies the reporter signal rather than the target sequence of interest that is to be detected. Thus, bDNA technology amplifies signal directly from captured target RNA without purification or reverse transcription. RNA quantitation is performed directly from a tissue sample. By measuring the nucleic acid at the sample source, the assay avoids variations or errors inherent to extraction and amplification of target polynucleotides. The QUANTIGENE® Plex hybridization-based Branched DNA (bDNA) signal amplification technology can be combined with multiplex bead based assay system such as the Luminex system described below to enable simultaneous detection of multiple pathogens of interest.

In brief, in an assay of the invention, a target nucleic acid to be detected is released from cells and captured by a Capture Probe (CP) on a solid surface (e.g., a well of a microtiter plate) through synthetic oligonucleotide probes called Capture Extenders (CEs). Each capture extender has a first polynucleotide sequence that can hybridize to the target nucleic acid and a second polynucleotide sequence that can hybridize to the capture probe. Typically, two or more capture extenders are used. Probes of another type, called Label Extenders (LEs), hybridize to different sequences on the target nucleic acid and to sequences on an amplification multimer. Additionally, Blocking Probes (BPs), which hybridize to regions of the target nucleic acid not occupied by CEs or LEs, are typically used to reduce non-specific target probe binding. A probe set for a given nucleic acid thus has CEs, LEs, and typically BPs for the target citrus pathogen. The CEs, LEs, and BPs are complementary to nonoverlapping sequences in the target nucleic acid from the citrus pathogen, and are typically, but not necessarily, contiguous.

Signal amplification begins with the binding of the LEs to the target mRNA. An amplification multimer is then typically hybridized to the LEs. The amplification multimer has multiple copies of a sequence that is complementary to a label probe (it is worth noting that the amplification multimer is typically, but not necessarily, a branched-chain nucleic acid; for example, the amplification multimer can be a branched, forked, or comb-like nucleic acid or a linear nucleic acid). A label, for example, alkaline phosphatase, is covalently attached to each label probe. (Alternatively, the label can be noncovalently bound to the label probes.) In the final step, labeled complexes are detected, e.g., by the alkaline phosphatase-mediated degradation of a chemilumigenic substrate, e.g., dioxetane. Luminescence is reported as relative light unit (RLUs) on a microplate reader. The amount of chemiluminescence is proportional to the level of mRNA expressed from the target gene.

The present invention provides a method and compositions for detecting the presence or absence of at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, or all nine of the citrus pathogens described herein. As explained above, detection is performed using bDNA signal amplification technology and capture extender probes and label extender probes that target the pathogen nucleic acid regions described herein. The general design of branched amplification assays, e.g., suitable amplification multimers, considerations in designing capture probes that bind to the capture extenders, etc.; configuration; and hybridization conditions for such reactions can be determined using methods known in the art (see, e.g., U.S. Patent Application Publication No. 20120003648 and the references cited therein).

Citrus Pathogen Probes

The nine pathogen targets and internal citrus gene were developed based on specific genomic sequences and characteristics in the pathogens' genome. The probes (Table 1) included Capture Extenders (CE), Label Extenders (LE), Blocking Probes (BL) as per manufacturer's recommendations were designed and developed based on the conserved sequences in the genome of each pathogen. CTV-Pan (universal) probes was designed based on the pathogen sequence alignment of CTV isolates worldwide and included all major CTV genotypes. CTV-T30 (mild strain) probes were designed based on the sequence alignment of worldwide T30 genotype isolates. CTV-VT probes were designed based on sequence alignment of worldwide CTV isolates having a VT genotype. Similarly, probes for CPV, CTLV, CLBV, CEVd, HSVd and CiLV were based on pathogen sequence alignment from data deposited in GenBank. In the present invention, the CE and LE probe sequences shown in Table 1 are the regions of the CE and LE oligonucleotides that target the pathogen.

The present invention employs CE and LE probes that comprise sequences presented in Table 1 or are variants of the sequences in Table 1 that retain the ability to hybridize to the same target nucleic acid sequence as the probes shown in Table 1 such that the presence of the pathogen in a plant sample can be detected. Such variant probe sequences typically have no more than 1, 2, 3, 4, 5, 6, 7, or 8 nucleotide changes relative to a probe sequence as shown in Table 1. In some embodiments, a variant probe useful in the invention comprises at least 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20, or more, contiguous nucleotides of a sequence shown in Table 1.

The methods and compositions for detecting one or more of the 9 citrus pathogens as described herein may also include probe to detect a control nucleic acid sequence. In some embodiments, the control is a housekeeping gene that is common to citrus plants. In some embodiments, the housekeeping gene is NADH dehydrogenase gene. In some embodiments, the CE and LE probes comprises the NAD sequences shown in Table 1 or are variants of the sequences that retain the ability to hybridize to the target region in the NAD sequence. In some embodiments, such a variant probe comprises at least 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20, or more, contiguous nucleotides of a sequence shown in Table 1; or has no more than 1, 2, 3, 4, 5, 6, 7, or 8 nucleotide changes relative to the sequence shown in Table 1.

In some embodiments, one or more blocking probes may be employed. Table 1 provides examples of sequences that may be employed in blocking probes useful in the invention.

In some embodiments, multiple capture extender and/or label extender probes shown in Table 1, or variants thereof as described herein, are used in the invention. In some embodiments, each of the probes that target a pathogen is shown in Table 1. In some embodiments, all of the probes, including any blocking probes, shown in Table 1, or variants thereof as described herein, for a given pathogen are used in the invention.

Plant Samples

The sample evaluated for the presence of citrus pathogens can be from any plant material (e.g., seed, foliage, limbs, trunk, bark, rootstock, fruit, germplasm, propagule, cuttings, and budwood). RNA is extracted using well known techniques. Such an RNA sample may also comprise DNA. Methods for extracting RNA from a plant samples are known to those skilled in the art and are described in Bilgin et al., Nature Protocols, 4:333-340, (2009); Berendzen et al., Plant Methods, 1:4 (2005); Elspeth MacRae, Methods in Molecular Biology, vol. 353: Protocols for Nucleic Acid Analysis by Nonradioactive Probes, Second Edition, Humana Press, New Jersey, 15-24, (2007). Non-limiting examples of commercially available plant RNA extraction kits include RNAeasy Plant Mini Kit (Qiagen, Hilden, Germany), PrepEase Plant Spin Kit (Affymetrix, Santa Clara, Calif.), Agilent Plant RNA Isolation Mini Kit (Agilent Technologies, Santa Clara, Calif.), Plant RNA Isolation Aid (Ambion, Austin, Tex.), and Spectrum Plant total RNA kit (Sigma-Aldrich, St. Louis, Mo.).

The following examples are offered to illustrate, but not to limit, the claimed invention.

EXAMPLES Example 1 High Throughput Assays for Rapid and Accurate 10-Plex Detection of Citrus Pathogens

The assay was developed using a QuantiGene Plex and Luminex based assay procedure. The probes used for detecting the pathogens are shown in Table 1.

TABLE 1 Sequence of specific probes including Capture Extenders (CE), Label  Extenders (LE), Blocking Probes (BL) designed and developed for the specific detection of nine citrus pathogen targets and a housekeeping  citrus gene as an internal control with QUANTIGENE® Plex hybridization  based Branched DNA (bDNA) signal amplification and Luminex based assay. Targets^(a) Probes Probe sequence (5′→3′) SEQ ID NO: CTV-Pan CTV001 CE ctccgcctgaaacactcagactc 1 (all major CTV CTV002 CE atgaagtggtgttcacggagaa 2 genotypes) CTV003 CE attttaaagactttacccatccggt 3 CTV004 CE ggttcacgcatacgttaagcc 4 CTV005 CE aacacacactctaaggagaacttcttt 5 CTV006 CE cccccatagggacagtgtgttgg 6 CTV007 LE gaacttattccgtccacttcaatcag 7 CTV008 LE aagggtttttaccaacccgacata 8 CTV009 LE tattgtctagtgatacatcaccatcat 9 CTV010 LE atatggttaattttcccctcgatc 10 CTV011 LE gggagcttagaccaacgagagg 11 CTV012 LE tcacttgagaccactaccactctgt 12 CTV-T30 (CTV- T30001 CE cgggtgaatttgaatcgaaatt 13 T30 genotype) T30002 CE ggatcgagctccggagata 14 T30003 CE ccaagtcccgcagggtcc 15 T30004 CE aaccgtctggttgggatttaca 16 T30005 CE tgtattgatattatgggcgtagaac 17 T30006 CE aagggacgatcggcccagcagcc 18 T30007 CE catacctccaagcgcccgcaa 19 T30008 CE tggggactttcacgcacagt 20 T30009 LE agcgaaagtcgaggacttgaa 21 T30010 LE cgaaattatgtaatcgctgcgtac 22 T30011 LE aggcgcgccagatgcg 23 T30012 LE tgcaggactccaacggtattaa 24 T30013 LE ggttgtatcagtgccgaagaag 25 T30014 LE gaaaactccttaaccaccgtagt 26 T30015 LE ttaatcgcgcgaacagca 27 T30016 LE aataggacgtccggcagct 28 T30017 LE cggagcgcggagcgtc 29 T30018 LE ggaggccacagaggcatc 30 T30019 LE acaccagatgtgtcgaaaacag 31 T30020 LE cagagcggggacgcacg 32 T30023 LE tcttcgccttgcgaatgga 33 T30024 LE ggctgagaaagaatgcagaatctt 34 T30025 LE cgagagaagagagaagaagccc 35 T30026 LE gtgccgcaagggacttcc 36 T30027 LE gcctgcgaagtctgtgacgc 37 T30028 LE agggtcaactagtttcgcaacac 38 T30029 BL gctagctccgagtttcgacatat 39 T30031 BL gcgcgaactgagaacgga 40 CTV-VT (CTV- VT002 CE ggacgtgatttccggaggg 41 VT genotype) VT003 CE accgattcccgcagcgt 42 VT004 CE ggcaatttgccgggatttac 43 VT005 CE atttgtttgtatgggcgtagtg 44 VT007 CE agaatacctccaaatgcccg 45 VT008 CE ggcgtcccttaagtttgatct 46 VT009 LE gaaagtcaaggacttgaagcg 47 VT010 LE tgatgtaatcgctgcgtacagc 48 VT011 LE gcgccagatgcgcgaga 49 VT012 LE gactccaacggtgttaaaggc 50 VT013 LE ggttgtttcagtaccgaagaagt 51 VT014 LE aaaattccttaaccaccttggt 52 VT015 LE ttaatcgcgcgaacagca 53 VT016 LE tgggacgtccggcagct 54 VT017 LE agagcgcggagcgtcaa 55 VT018 LE ggaggccacagaggcatcc 56 VT019 LE cgacaccagatgtgtcgataacag 57 VT020 LE cgacagagcggggacgta 58 VT021 LE gcagtaaggggaggtttacacag 59 VT022 LE tggacttcttggcggcg 60 VT023 LE tctttcttcgccttgcgaa 61 VT024 LE ccggctaagaaagaaagcagaa 62 VT025 LE cgtgccgcaggggactt 63 VT026 LE gcgcctacgaagtctatgacg 64 VT027 LE atggtagggtctactcgtttcataac 65 VT028 LE cgtcttggggactctcgtgc 66 VT029 BL agctccgagtttcgacatgttat 67 VT030 BL aaacaggatttccgtagaggg 68 VT031 BL gcgcgaacagaaaacgga 69 VT032 BL cccgtgagaagagtgaagaagc 70 Psorosis (CPsV) psoro001 CE tggcgatggtgaagggcc 71 psoro002 CE aagaacaaggggtttcagaatgatag 72 psoro003 CE agcctcactccagatggcaga 73 psoro004 CE tcaattgcaataagagattttctgaa 74 psoro005 CE ctcctgaatccctgatgccatt 75 psoro006 CE atctgtgagatatgctgggtttgc 76 psoro007 CE aacaaagaaattccctgcaaggg 77 psoro008 CE gtgaggaattgagccatgctcc 78 psoro009 LE catggagtgtgttgacaaaacca 79 psoro010 LE attgacatggccgagaggataataa 80 psoro011 LE aaaaggcttcatcctttatctgatga 81 psoro012 LE tggagggacaatggaagaatcag 82 psoro013 LE gctggaaaccaatcaaaagattgaaaaa 83 psoro014 LE gtcccctgctgttggtgcaa 84 psoro015 LE tgtttctcaagattgatatagacaactt 85 psoro016 LE gaagctgtatgatggtgatgtaagttt 86 CTLV CTLV001 CE tgctgagagggacctaaatcctct 87 CTLV002 CE gggaggaaccgtcagaagttcc 88 CTLV003 CE gtgattgcagagaagaaggtaaagctc 89 CTLV004 CE aagaaattcacgagccaaatcagc 90 CTLV005 CE caaaagctttgggccatttctt 91 CTLV006 CE cctgcctcgaaaaccccttt 92 CTLV007 LE tgttgaagcacgtcttccaaactcat 93 CTLV008 LE gaaactgggtcttatcagatgaccc 94 CTLV009 LE agaagtagcagcaaaggttttcaattc 95 CTLV010 LE ttgtccttcagtacgaaaaagcct 96 CTLV011 LE cgactcctaaccctccagttcca 97 CTLV012 LE cctgcaagaccgcgaccaa 98 CTLV013 LE ttaagtataaaggcaggcatgtcaa 99 CLBV CLBV001 CE cagctctgaattttcgaatgatgtca 100 CLBV002 CE ttgagtgactcattcaattcttcaa 101 CLBV003 CE cccagccaaaattgcagct 102 CLBV004 CE atctttgggaaatgtctttcaact 103 CLBV005 CE gctcatgccctttttttttcaaatt 104 CLBV006 LE tgaggaatggttcaactatggct 105 CLBV007 LE tcagaatttctgtcctcatcagatg 106 CLBV008 LE tctccatgctcggccacta 107 CLBV009 LE tcagggtccacctcctctgtg 108 CLBV010 LE tgtgatctcaagctgtgatgcat 109 CLBV011 LE ttcaagctgctgctctctatctgc 110 CLBV012 LE ccactgccggtcagtggtt 111 CLBV013 LE cagcatgtaccggttcagaagat 112 CLBV014 LE actgtggagcgtgtgctgatt 113 CLBV015 LE gcagatcattcaccacatgca 114 CLBV016 BL ggaaaaaatggcgaagaagacc 115 CLBV017 BL ctttttttgaataaactctgccgtac 116 CLBV018 BL tgtttctcagatcttctgcttctgc 117 CEVd CEVd001 CE tcttttttcttttcctgcctgc 118 CEVd002 CE ggatccctgaaggacttctt 119 CEVd003 CE tcctccaggtttccccgg 120 CEVd004 CE ttctccgctggacgccag 121 CEVd005 CE cctcgcccggagagcagt 122 CEVd006 CE tagggttccgagggctttcac 123 CEVd007 LE ggaacctcaagaaagatcccg 124 CEVd008 LE agggtcaggtgagcaccaca 125 CEVd009 LE cccccccgacctcgact 126 CEVd010 LE tgatccgcggcgaccg 127 CEVd011 LE aaaggaaggagacgagctcctgt 128 CEVd012 LE ggatgtggagccagcagcg 129 CEVd013 LE tcagttgtttccaccgggtagt 130 CEVd014 LE gcggtttggggttgaagct 131 HSVd CVdII001 CE ttttctttgcttgcccatgc 132 CVdII002 CE ggattctgagaagagttgcccc 133 CVdII003 CE agctagaagcctctactccagagc 134 CVdII004 CE ggacgatcgatggtgtttcga 135 CVdII005 CE agccaggagaaggtaaaagaagaag 136 CVdII006 CE cgaaccgagaggtgatgcca 137 CVdII007 LE ggcaactcgagaattccccag 138 CVdII008 LE ggggctcctttctcaggtaagt 139 CVdII009 LE accgcggccctctctcc 140 CVdII010 LE ccggtcgcgtctcatcgga 141 CVdII011 LE ggcagaggctcagatagacaaaaa 142 CVdII012 LE gggctcaagagaggatccgc 143 Leprosis (CiLV) leprosis3|CE tgctaatatcacgcagaccttca 144 leprosis9|CE ggccttctgcttagcaggttt 145 leprosis11|CE tgggtggagcaagctgctt 146 leprosis14|CE cggcatattttgggcagtg 147 leprosis18|CE gcttccattaccttaaaatcaggta 148 leprosis19|CE gacggcaactaggtcctcagaa 149 leprosis1|LE ctcaatggcctgcataatctca 150 leprosis2|LE ggaacagacacgttgtgccg 151 leprosis4|LE actgctgcttcttcttagtaggct 152 leprosis5|LE gtgacagttgttgaggttgcg 153 leprosis7|LE ccgggttgcagttgctgag 154 leprosis8|LE cttggcctgataaccactagga 155 leprosis16|LE ttataatatgtcatccctatctgcttc 156 leprosis17|LE acgcatagggctcggatatc 157 leprosis21|LE atactatataagcgcttctcaaagct 158 leprosis22|LE gtcgcttcgggaagccc 159 leprosis23|LE ccgggacaacgttctttatgg 160 leprosis24|LE caatgtagtgatcactgaactcgaata 161 Nad5 Nad54|CE ggtcattatagcggttccttctga 162 Nad55|CE gaagagaatgaaacgcacgtagt 163 Nad59|CE caaacatttccgatgagatcca 164 Nad515|CE aataacacataaatcgagggctatg 165 Nad519|CE aaatatgaagcaagacctactccct 166 Nad522|CE ctcgattgacaggcatagcttt 167 Nad51|LE gggcaaaaatacgataagtagataca 168 Nad52|LE ctgctacggaactaccgagaag 169 Nad56|LE tcataaaaagcaatcagagataagatc 170 Nad57|LE actagctcccggtgcgact 171 Nad510|LE caagaagccccaagaagcat 172 Nad511|LE actacggtcgggctatcgaa 173 Nad512|LE cttatggatgtaaccacaattaacatc 174 Nad513|LE tggaataaagatggaccaagcta 175 Nad517|LE gagagttatctccagtcaccaacat 176 Nad518|LE cccatcccaggaataattgaa 177 Nad520|LE gtcgtgtaaaccagaaatgaattaac 178 Nad521|LE tgtagctgctttatctgcctgaa 179 ^(a)CTV-Pan: Citrus tristeza virus major genotypes (universal), CTV-T30: CTV genotype T30, CTV-VT: CTV genotype VT, Psorosis: Citrus psorosis virus (CPsV), CTLV: Citrus tatter leaf virus, CLBV: Citrus leaf blotch virus, CEVd: Citrus exocortis viroid, HSVd: Hop stunt viroid (syn. citrus viroid IIa, IIb, and IIc), Leprosis: Citrus leprosis virus (CiLV), Nad5: NADH dehydrogenase gene, a housekeeping citrus gene, used as an internal control.

The procedure from the QUANTIGENE® Plex 2.0 hybridization-based Branched DNA (bDNA) signal amplification Assay User Manual from Affymetrix/Panomics Inc is shown below:

Capturing Target RNA from Total, Purified, In Vitro Transcribed RNA or Total Nucleic Acid

1. Sample and reagent preparation: thaw probe set, blocking reagent and total nucleic acid samples (both RNA and DNA or RNA only), and place them on ice.

2. Pre-warm lysis mixture at 37° C. for 30 minutes.

3. Prepare a working bead mix including nuclease-free water, lysis mixture, blocking reagent, capture beads, probe set, according to reaction composition (Table 2).

TABLE 2 Working Bead Mix Set Up Order of addition Reagent Per well (μl) 1 Nuclease-free water 38.7 2 Lysis mixture 33.3 3 Blocking reagent 2 4 Capture beads 1 5 Probe set 5 Total 80 4. Vortex working bead mix for 30 sec, transfer 80 μl to each well of the hybridization plate. 5. Add 20 μl nucleic acid samples (or RNA sample) to each well of the above plate. 6. Seal the hybridization plate with a pressure seal and mount the plate into the shaking incubator. 7. Incubate for 18-22 hours at 54° C. at 600 rpm. Signal Amplification and Detection of RNA Targets 1. Place label probe diluent and SAPE diluent to room temperature. Incubate amplifier diluent at 37° C. for 20 minutes. 2. Prepare 200 ml wash buffer including 0.6 ml wash buffer Component 1, 10 ml wash buffer Component 2 and 189.4 ml nuclease-free water. 3. Add 36 μl pre-amplifier to 12 ml amplifier diluent. 4. Take the hybridization plate out of the shaking incubator, and spin at 240 g for 60 seconds. 5. Open the pressure seal, mix with pipette, then transfer the hybridization mixture to the magnetic separation plate. 6. Put the magnetic separation plate on the plate holder of the plate washer for 60 seconds, then empty the magnetic separation and wash three times with 100 μl wash buffer. 7. Add 100 μl pre-amplifier solution to each well. 8. Seal the magnetic separation plate with a foil plate seal and shake for 60 minutes at 50° C. with 600 rpm. 9. Add 36 μl amplifier to 12 ml amplifier diluent. 10. Take the magnetic separation plate out of the shaking incubator. 11. Open the foil plate seal. 12. Put the magnetic separation plate on the plate holder of the plate washer for 60 seconds, then empty the magnetic separation plate and wash three times with 100 μl wash buffer. 13. Add 100 μl amplifier solution to each well. 14. Seal the magnetic separation plate with a foil plate seal and shake for 60 minutes at 50° C. with 600 rpm. 15. Add 36 μl label probe to 12 ml label probe diluent. 16. Take the magnetic separation plate out of the shaking incubator and open the foil plate seal. 17. Put the magnetic separation plate on the plate holder of the plate washer for 60 seconds, then empty the magnetic separation plate and wash three times with 100 μl wash buffer. 18. Add 100 μl label probe solution to each well. 19. Seal the magnetic separation plate with a foil plate seal and shake for 60 minutes at 50° C. with 600 rpm. 20. Add 36 μl SAPE to 12 ml SAPE diluent. 21. Take the magnetic separation plate out of the shaking incubator and open the foil plate seal. 22. Put the magnetic separation plate on the plate holder of the plate washer for 60 seconds, then empty the magnetic separation plate and wash three times with 100 μl wash buffer. 23. Add 100 μl SAPE solution to each well. 24. Seal the magnetic separation plate with a foil plate seal and shake for 30 minutes at 50° C. with 600 rpm. 25. Take the magnetic separation plate out of the shaking incubator, open the foil plate seal. 26. Put the magnetic separation plate on the plate holder of the plate washer for 60 seconds, then empty the magnetic separation plate and wash three times with 100 μl SAPE wash buffer. 27. Add 130 μl SAPE wash buffer to each well. 28. Seal the magnetic separation plate with a foil plate seal and cover the magnetic separation plate with foil and shake for 2-3 minutes at room temperature with 600 rpm, then use Luminex instrument to read.

Initially, the assay was performed using nine samples from healthy and infected citrus plants with CTV genotype T30, CTV genotype VT, CPsV (Psorosis), CTLV, CLBV, CEVd, HSVd, CiLV (Leprosis), respectively (FIG. 1). A procedure for high throughput robotic extraction and purification of nucleic acid targets, optimized for citrus tissues, was developed and used with the Luminex-based QUANTIGENE® Plex hybridization-based Branched DNA (bDNA) signal amplification system to increase uniformity and cost effectiveness of the test. Sample CTV-T30 was detected to show positive reactions with both CTV-Pan and CTV-T30, but not CTV-VT and other pathogen targets. In addition, sample CTV-T30 was detected to show positive reactions with Nad5, the positive internal control for citrus plants, which could be used to access the RNA extraction quality and to normalize data for accurate quantification of the pathogen populations among samples. Sample CTV-VT was confirmed to have CTV genotype VT and HSVd from other studies. In contrast to sample CTV-T30, CTV-VT was detected to show positive reactions with Nad5, CTV-Pan, CTV-VT, and HSVd, but not CTV-T30 and the other RNA pathogen targets. Sample HSVd showed positive reactions with Nad5 and HSVd, but not other pathogen targets. Similarly, samples CEVd, CPsV and CTLV showed positive reactions with Nad5 and their pathogen targets, respectively, but not other pathogen targets. Sample CLBV was confirmed to have HSVd and CLBV from other studies. In the assay, sample CLBV showed positive reactions with Nad5, CLBV and HSVd, but not other pathogen targets. Sample Leprosis was confirmed to have CTV, HSVd and Psorosis from other studies. In the assay, sample Leprosis showed positive reactions with Leprosis, Nad5, CTV-Pan, CTV-T30, CTV-VT, and HSVd. Finally, the healthy Navel sweet orange control sample showed positive reaction with Nad5 but not to any pathogen targets. These data showed that the assay is capable of specific detection of each target including Nad5, CTV-Pan, CTV genotype T30, CTV genotype VT, Psorosis, CTLV, CLBV, CEVd, HSVd, and Leprosis.

Developmental assays were performed using more CTV samples from healthy and infected citrus plants (FIG. 2). Every sample tested had a positive reaction with Nad5 indicating that nucleic acid extracted per plant was effective. In addition, sample CTV-1 containing CTV genotype T30 showed positive reactions with both CTV-Pan and CTV-T30, but not CTV-VT. Sample CTV-2 containing CTV genotype VT showed positive reactions with both CTV-Pan and CTV-VT, but not CTV-T30. Sample CTV-3 containing CTV genotype T36 showed positive reaction with CTV-Pan only, but not to CTV-T30 or CTV-VT. Lastly, samples 4 and 5 containing both T30 and VT genotypes showed positive reactions with CTV-Pan, CTV-T30 and CTV-VT. These data further validate the 10-plex detection system could detect broad-spectrum CTV strains but also the major genotypes T30 and VT.

The assay was also performed using healthy citrus and citrus infected with citrus viroids (FIG. 3). There are seven known distinct viroid species representing four genera in the Pospiviroidae family. They are: Citrus exocortis viroid (CEVd, genus Pospiviroid), Hop stunt viroid (HSVd, genus Hostuviroid), Citrus bark cracking viroid (CBCVd, genus Cocadviroid) and Citrus bent leaf viroid (CBLVd), Citrus dwarfing viroid (CDVd), Citrus viroid V (CVd-V) and CVd-VI of the genus Apscaviroid. Collectively, these various citrus viroids cause abnormal growth. All samples tested were positive for Nad5 and demonstrated good quality nucleic acid extraction and purification. Viroid-3, -5 and -7 contained HSVd and showed positive reaction with HSVd but not CEVd. Viroid-6 contained CEVd and showed a positive reaction with CEVd but not HSVd. Samples infected with known multiple viroid species were also tested in the assay. Sample viroid-2 contained CEVd and CBCVd and showed a positive reaction with CEVd, but not HSVd. Sample viroid-4 containing CBLVd, HSVd, CDVd, CBCVd, CVd-V and CEVd showed positive reactions with both CEVd and HSVd. In short, it was further validated that the 10-plex detection system could detect specifically different citrus viroid species CEVd and HSVd, respectively.

The high throughput robotic extraction and purification of nucleic acid targets, optimized for citrus tissues, it showed that samples obtained from fresh or frozen tissue crude extraction using QUANTIGENE® hybridization-based Branched DNA (bDNA) signal amplification sample processing kit were consistently detected. Finally, sensitivity studies using serial dilutions of CTV and HSVd samples, respectively, suggested that those samples, obtained by the high throughput robotic extraction and purification of nucleic acid targets, were consistently detected after dilution of up to 1000 times.

All publications, patents, accession numbers, and patent applications cited in this specification are herein incorporated by reference as if each individual publication or patent application were specifically and individually indicated to be incorporated by reference.

Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be readily apparent to those of ordinary skill in the art in light of the teachings of this invention that certain changes and modifications may be made thereto without departing from the spirit or scope of the appended claims. 

What is claimed is:
 1. A method for detecting the presence or absence of nine citrus pathogens Citrus tristeza virus (CTV) universal, CTV genotype T30, CTV genotype VT, Citrus psorosis virus, Citrus tatter leaf virus, Citrus leaf blotch virus, Citrus exocortis viroid, Hop stunt viroid, and Citrus leprosis virus in a plant sample, the method comprising: extracting RNA from said sample; performing a multiplex branched DNA signal amplification reaction; wherein the reaction comprises a probe set that targets Citrus tristeza virus (CTV) universal, a probe set that targets CTV genotype T30, a probe set that targets CTV genotype VT, a probe set that targets Citrus psorosis virus, a probe set that targets Citrus tatter leaf virus, a probe set that targets Citrus leaf blotch virus, a probe set that targets Citrus exocortis viroid, a probe set that targets Hop stunt viroid, and a probe set that targets Citrus leprosis virus, wherein each probe set comprises at least one capture extender probe and a at least one label extender probe, and wherein; the at least one capture extender probe that targets CTV universal comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:1, 2, 3, 4, 5, or 6; and the at least one label extender probe that targets CTV universal comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO: 7, 8, 9, 10, 11, or 12; the at least one capture extender probe that targets CTV genotype T30 comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:13, 14, 15, 16, 17, 18, 19, or 20; and the at least one label extender probe that targets CTV genotype T30 comprises at least 8, 9, or 10 contiguous of a probe sequence of SEQ ID NO:21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, or 38; the at least one capture extender probe that targets CTV VT genotype comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:41, 42, 43, 44, 45, or 46; and the at least one label extender probe that targets CTV VT genotype comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, or 66; the at least one capture extender probe that targets Citrus psorosis virus comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:71, 72, 73, 74, 75, 76, 77, or 78; and the at least one label extender probe that targets Citrus psorosis virus comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:79, 80, 81, 82, 83, 84, 85, or 86; the at least one capture extender probe that targets Citrus tatter leaf virus comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:87, 88, 89, 90, 91, or 92; and the at least one label extender probe that targets Citrus tatter leaf virus comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:93, 94, 95, 96, 97, 98, or 99; the at least one capture extender probe that targets Citrus leaf blotch virus comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:100, 101, 102, 103, or 104; and the at least one label extender probe that targets Citrus leaf blotch virus comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:105, 106, 107, 108, 109, 110, 111, 112, 113, or 114; the at least one capture extender probe that targets Citrus exocortis virus comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:118, 119, 120, 121, 122, or 123; and the at least one label extender probe that targets Citrus exocortis virus comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:124, 125, 126, 127, 128, 129, 130, or 131; the at least one capture extender probe that targets Hop stunt viroid comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:133, 134, 135, 136, or 137; and the at least one label extender probe that targets Hop stunt viroid comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:138, 139, 140, 141, 142, or 143; the at least one capture extender probe that targets Citrus leprosis virus comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:144, 145, 146, 147, 148, or 149; and the at least one label extender probe that targets Citrus leprosis virus comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, or 161; and detecting the presence or absence of a signal above background from at least one of the probe sets, wherein the presence of the signal is indicative of the presence of the pathogen that the probe set targets.
 2. The method of claim 1, wherein the reaction comprises multiple capture extender probes and multiple label extender probes that target each of the nine pathogens, wherein: each of the multiple capture extender probes that target CTV universal comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:1, 2, 3, 4, 5, or 6; and each of the label extender probes that target CTV universal comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO: 7, 8, 9, 10, 11, or 12; each of the multiple capture extender probes that target CTV genotype T30 comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:13, 14, 15, 16, 17, 18, 19, or 20; and each of the multiple extender probes that target CTV genotype T30 comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, or 38; each of the multiple capture extender probes that target CTV VT genotype comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:41, 42, 43, 44, 45, or 46; and each of the multiple label extender probes that target CTV VT genotype comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, or 66; each of the multiple capture extender probes that target Citrus psorosis virus comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:71, 72, 73, 74, 75, 76, 77, or 78; and each of the multiple extender probes that target Citrus psorosis virus comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:79, 80, 81, 82, 83, 84, 85, or 86; each of the multiple capture extender probes that target Citrus tatter leaf virus comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:87, 88, 89, 90, 91, or 92; and each of the multiple label extender probes that target Citrus tatter leaf virus comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:93, 94, 95, 96, 97, 98, or 99; each of the multiple capture extender probes that target Citrus leaf blotch virus comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:100, 101, 102, 103, or 104; and each of the multiple label extender probes that target Citrus leaf blotch virus comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:105, 106, 107, 108, 109, 110, 111, 112, 113, or 114; each of the multiple capture extender probes that target Citrus exocortis virus comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:118, 119, 120, 121, 122, or 123; and each of the multiple label extender probes that target Citrus exocortis virus comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:124, 125, 126, 127, 128, 129, 130, or 131; each of the multiple capture extender probes that target Hop stunt viroid comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:133, 134, 135, 136, or 137; and each of the multiple label extender probes that target Hop stunt viroid comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:138, 139, 140, 141, 142, or 143; each of the multiple capture extender probes that target Citrus leprosis virus comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:144, 145, 146, 147, 148, or 149; and each of the multiple label extender probes that target Citrus leprosis virus comprises at least 8, 9, or 10 contiguous nucleotides of a probe sequence of SEQ ID NO:150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, or
 161. 3. The method of claim 1, wherein the reaction comprises at least one blocking probe for the corresponding pathogen, wherein the at least one blocking probe has a sequence set forth in SEQ ID NO:39, 40, 67, 68, 69, 70, 115, 116, or
 117. 4. The method of claim 1, wherein the reaction further comprises using at least one capture extender probes and at least one label extender probes for Nad5, wherein the at least one capture extender probe has a sequence set forth in SEQ ID NO:162, 163, 164, 165, 166, or 167; and the last least one label extender probe has a sequence set forth in SEQ ID NO:168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, or
 179. 5. The method of claim 1, wherein the plant sample is from seed, foliage, limbs, trunk, bark, rootstock, fruit, germplasm, propagule, cuttings, or budwood.
 6. The method of claim 2, wherein: the multiple capture extender probes that target CTV universal comprise probes having the sequences of SEQ ID NO:1, 2, 3, 4, 5, and 6; and the multiple label extender probes that target CTV universal comprise probes having the sequences of SEQ ID NO: 7, 8, 9, 10, 11, and 12; the multiple capture extender probes that target CTV genotype T30 comprise probes having the sequences of SEQ ID NO:13, 14, 15, 16, 17, 18, 19, and 20; and the multiple label extender probes that target CTV genotype T30 comprise probes having the sequences of SEQ ID NO:21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, and 38; the multiple capture extender probes that target CTV VT genotype comprise probes having the sequences of SEQ ID NO:41, 42, 43, 44, 45, or 46; and the multiple label extender probes that target CTV VT genotype comprise probes having the sequences of SEQ ID NO:47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, and 66; the multiple capture extender probes that target Citrus psorosis virus comprise probes having the sequences of SEQ ID NO:71, 72, 73, 74, 75, 76, 77, and 78; and the multiple label extender probes that target Citrus psorosis virus comprise probes having the sequences of SEQ ID NO:79, 80, 81, 82, 83, 84, 85, and 86; the multiple capture extender probes that target Citrus tatter leaf virus comprise probes having the sequences of SEQ ID NO:87, 88, 89, 90, 91, and 92; and the multiple label extender probes that target Citrus tatter leaf virus comprise probes having the sequences of SEQ ID NO:93, 94, 95, 96, 97, 98, and 99; the multiple capture extender probes that target Citrus leaf blotch virus comprise probes having the sequences of SEQ ID NO:100, 101, 102, 103, and 104; and the multiple label extender probes that target Citrus leaf blotch virus comprise probes having the sequences of SEQ ID NO:105, 106, 107, 108, 109, 110, 111, 112, 113, and 114; the multiple capture extender probes that target Citrus exocortis virus comprise probes having the sequences of SEQ ID NO:118, 119, 120, 121, 122, and 123; and the multiple label extender probes that target Citrus exocortis virus comprise probes having the sequences of SEQ ID NO:124, 125, 126, 127, 128, 129, 130, and 131; the multiple capture extender probes that target Hop stunt viroid comprise probes having the sequences of SEQ ID NO:133, 134, 135, 136, and 137; and the multiple label extender probes that target Hop stunt viroid comprise probes having the sequences of SEQ ID NO:138, 139, 140, 141, 142, and 143; the multiple capture extender probes that target Citrus leprosis virus comprise probes having the sequences of SEQ ID NO:144, 145, 146, 147, 148, and 149; and the multiple label extender probes that target Citrus leprosis virus comprise probes having the sequences of SEQ ID NO:150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, and
 161. 7. The method of claim 2, wherein the reaction further comprises at least one blocking probe for the corresponding pathogen, wherein the at least one blocking probe has a sequence set forth in SEQ ID NO:39, 40, 67, 68, 69, 70, 115, 116, or
 117. 8. The method of claim 6, wherein the reaction further comprises multiple blocking probes, wherein the multiple blocking probes have the sequences of SEQ ID NO:39, 40, 67, 68, 69, 70, 115, 116, and
 117. 9. The method of claim 2, wherein the reaction further comprises at least one of the capture extender probes and at least one of the label extender probes for Nad5, wherein the at least one capture extender probe has a sequence set forth in SEQ ID NO:162, 163, 164, 165, 166, or 167; and the last least one label extender probe has a sequence set forth in SEQ ID NO:168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, or
 179. 10. The method of claim 6, wherein the reaction further comprises multiple capture extender probes for Nad5 and multiple label extender probes for Nad 5, wherein the multiple capture extender probes for Nad 5 comprise probes having the sequences set forth in SEQ ID NO:162, 163, 164, 165, 166, and 167; and the multiple label extender probes for Nad 5 comprise probes have the sequences set forth in SEQ ID NO:168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, and
 179. 